Phylogenetic Relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) Species in the Eastern Mediterranean Inferred from Mitochondrial DNA, with Emphasis on Iranian Species

Biogeography of rodents in Iran: species richness, elevational distribution and their environmental correlates

Rodent biogeographic studies are disproportionately scarce in Iran, however, they are an ideal system to understand drivers of biodiversity distributions in the country. The aims of the present research are to determine (i) the pattern of rodent richness across the country, (ii) quantify their elevational distribution patterns, and (iii) explore the underlying mechanisms. To reach these goals, an updated species list was compiled based on the latest taxonomic revisions, published until December 2021. We mapped all 76 rodent species distributions to develop the first map of rodent richness in Iran. We furthermore investigated their elevational distribution patterns in the following four geographic regions based on 100 m intervals; the Zagros Mountains, north of Alborz Mountains, south of Alborz and Kopet-Dagh mountains, and central and east mountains. North-east of Iran, Zagros Mountains, Alborz Mountains, and northwestern of Iran showed the highest richness and were identified as biodiversity hotspots of rodents in the country. This study highlights the importance of past climate change as the key driver of rodent richness in Iran. We showed that rodents’ elevational distribution patterns differ among geographic regions. Areas and elevational zones with the highest species richness should be prioritized for the conservation planning of rodents in Iran.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia

Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.

A taxonomic revision of fat dormice, genus Glis (Rodentia)

We address in this study the taxonomic status of the two major phylogenetic lineages of fat dormice, genus Glis. These lineages show unique mutations at 43 positions of the cytochrome b alignment and are classified as two distinct species, the European fat dormouse Glis glis (Linnaeus, C. [1766]. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis synonymis, locis, Vol. 1. Laurentii Salvii, Holmiae [Stockholm]) and the Iranian fat dormouse Glis persicus (Erxleben, I.C.P. [1777]. Systema regni animalis per classes, ordines, genera, species, varietates cum synonymia et historia animalium. Classis I. Mammalia. Impensis Weygandianis, Lipsia [Leipzig]). The European dormouse is widespread in Europe, Asia Minor and the Caucasus, while the Iranian dormouse occupies the southern Caspian coast in Iran. Ranges are presumably delimited in Azerbaijan by rivers Kura and Aras. The two species differ categorically in size of the glans penis, size and shape of the baculum and in width of the posterior extension of the premaxilla. The Iranian fat dormouse has on average a more blackish distal half of the tail, a higher count for abdominal nipples, and a longer maxillary tooth-row. Intraspecific structuring in G. glis indicates a taxonomic complexity which is not yet understood and requires a comprehensive systematic revision. To define the nominal taxon objectively we designate voucher PMS 27369 (Slovenian Museum of Natural History) as the neotype for G. glis, therefore restricting the type locality for the species to Mt. Krim in Slovenia.

Assessment differentiation degree cryptic species of the genus Apodemus in the Northern Caucasus based on non-metric cranial characters

A phenetic analysis of non-metric cranial traits of two genetically identified cryptic species of the genus Apodemus in different ecological conditions of the North Caucasus was carried out. The maximum distance obtained between cryptic species did not exceed the level of subspecies differences. The phenetic distance between A. uralensis and A. flavicollis, which inhabit symbiotopically and sympatrically in the Western Caucasus, is almost 2 times lower. The smaller value of phenetic differences is probably related to the habitat of both species in similar land-scapebiotopic and climatic conditions, which contributes to the development of phenotypic similarity. In general, the obtained results indicate weak morphological differentiation of the studied species according to the studied phenetic characters (cranial foramen), although according to the results of molecular genetic analysis of the cyt b gene site, the genetic distance between the studied taxa is 10% and corresponds to the level of interspecific differences. Based on the above, reliable diagnosis of the studied species in the Caucasus is possible only by molecular genetic methods.

Evolutionary history of water voles revisited: confronting a new phylogenetic model from molecular data with the fossil record

Recent water voles (genus Arvicola) display a prominent morphological diversity with a strong ecotypical background but with unclear taxonomic associations. We provide a novel synthetic view on the evolutionary history and the current taxonomic richness in the genus. Our molecular reconstruction, based on a 1143-bp-long sequence of cytochrome b and a 926-bp interphotoreceptor retinoid binding protein (irbp) confirmed the monophyly of four species (amphibius, sapidus, monticola and italicus) recognized thus far, and retrieved a new deeply divergent lineage from West Iran. Genetic divergence of the Iranian lineage (>9.0%) is inside the range of interspecies distances, exceeding the interspecies divergences between the remaining Arvicola species (range, 4.3–8.7%). The oldest name available for the Iranian phylogroup is Arvicola persicus de Filippi, 1865, with the type locality in Soltaniyeh, Iran. The molecular clock suggests the divergence of A. persicus in the Early Pleistocene (2.545 Ma), and the current radiation of the remaining species between 1.535 Ma (Arvicola sapidus) and 0.671 Ma. While A. sapidus possibly evolved from Arvicola jacobaeus, a fossil ancestor to A. persicus is unknown. The aquatic life-style of Mimomys savini, a direct ancestor to some fossil Arvicola, is retained in recent stem species A. sapidus and A. persicus, while a major shift toward fossorial morphotype characterizes the terminal lineages (amphibius, italicus and monticola). We suggest that habitat-dependent morphological plasticity and positive enamel differentiation in Arvicola amphibius widened its ecological niche that might trigger a range expansion across c. 12 million km2, making it one of the largest among arvicolines.

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

Background

Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.

Results

Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise F_ST<0.086.

Conclusion

Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

Mice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.

Hantavirus infection in Iranian patients suspected to viral hemorrhagic fever

BACKGROUND

Hantaviruses are a group of emerging pathogens causing hemorrhagic fever with renal syndrome and Hantavirus cardiopulmonary syndrome in human. This study was conducted to investigate Hantavirus infection among Iranian viral hemorrhagic fever suspected patients.

METHODS

From April 2014 to June 2016, 113 cases from 25 different provinces of Iran were analyzed for Hantavirus infection by IgM/IgG ELISA and pan-Hantavirus RT-PCR tests.

RESULTS

Although, viral genome was detected in none of the subjects, IgM and IgG antibodies were detected in 19 and 4 cases, respectively. Differentiation of the anti-Hantavirus antibodies according to virus species by EUROLINE Anti-Hantavirus Profile Kit revealed three Puumala virus IgM positive, one Hantaan virus IgM positive, one Hantaan virus IgM borderline, and two Puumala virus IgG borderline cases.

CONCLUSIONS

This study demonstrates the circulation of Hantaviruses in Iran and calls for further investigations of these life-threatening viruses in the country.

A survey on endoparasites in wild rodents of the Jaz Murian depression and adjacent areas, southeast of Iran

In this survey, rodents and their endoparasites were investigated in the Jaz Murian depression and adjacent areas, southeast Iran. In total, 146 specimens of rodents belong to 13 species were trapped. In general, 10 different genera of endoparasites including 11 species were collected. The endoparasites were identified as follows: (1) Nematodes: Trichuris muris, Syphacia obvelata, Labiostomum sp., Labiostomum naimi, Mastrophorus muris, Aspicularis tetraptera and Heligmosomoides skrjabini, Physaloptera sp. (2) Cestodes: Choanotaenia sp., Raillietina sp., and Hymenolepis diminuta. Of 146 captured rodents, Tatera indica was found with high parasitic infestation (with 93% infested) comparing to Acomys dimidiatus (66%), Rattus rattus (50%), Meriones libycus (15%), Jaculus blanfordi (14%) and Mus musculus (8%) whereas, seven rodent species, Nesokia indica, Gerbillus nanus, Golunda ellioti, Calomyscus hotsoni, Apodemus witherbyi, Cricetulus migratorius and Microtus mystacinus were free from any parasitic infestation. Those six infested rodent species were collected from the center of the Jaz Murian depression, whereas seven non-infested rodents' species except N. indica and G. nanus live in the marginal ranges of the Jaz Murian depression, therefore, these species inhabiting the central parts were supposed to be more important from the health aspect. The species, Labiostomum naimi collected from A. dimidiatus is the first report of this species in rodents from Iran.

Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice

A degree of host specificity, manifested by the processes of host-parasite cospeciations and host switches, is assumed to be a major determinant of parasites' evolution. To understand these patterns and formulate appropriate ecological hypotheses, we need better insight into the coevolutionary processes at the intraspecific level, including the maintenance of genetic diversity and population structure of parasites and their hosts. Here, we address these questions by analyzing large-scale molecular data on the louse Polyplax serrata and its hosts, mice of the genus Apodemus, across a broad range of European localities. Using mitochondrial DNA sequences and microsatellite data, we demonstrate the general genetic correspondence of the Apodemus/Polyplax system to the scenario of the postglacial recolonization of Europe, but we also show several striking discrepancies. Among the most interesting are the evolution of different degrees of host specificity in closely related louse lineages in sympatry, or decoupled population structures of the host and parasites in central Europe. We also find strong support for the prediction that parasites with narrower host specificity possess a lower level of genetic diversity and a deeper pattern of interpopulation structure as a result of limited dispersal and smaller effective population size.

Rodent-borne diseases and their public health importance in Iran

Background

Rodents are reservoirs and hosts for several zoonotic diseases such as plague, leptospirosis, and leishmaniasis. Rapid development of industry and agriculture, as well as climate change throughout the globe, has led to change or increase in occurrence of rodent-borne diseases. Considering the distribution of rodents throughout Iran, the aim of this review is to assess the risk of rodent-borne diseases in Iran.

Methodology/Principal finding

We searched Google Scholar, PubMed, Science Direct, Scientific Information Database (SID), and Magiran databases up to September 2016 to obtain articles reporting occurrence of rodent-borne diseases in Iran and extract information from them. Out of 70 known rodent-borne diseases, 34 were reported in Iran: 17 (50%) parasitic diseases, 13 (38%) bacterial diseases, and 4 (12%) viral diseases. Twenty-one out of 34 diseases were reported from both humans and rodents. Among the diseases reported in the rodents of Iran, plague, leishmaniasis, and hymenolepiasis were the most frequent. The most infected rodents were Rattus norvegicus (16 diseases), Mus musculus (14 diseases), Rattus rattus (13 diseases), Meriones persicus (7 diseases), Apodemus spp. (5 diseases), Tatera indica (4 diseases), Meriones libycus (3 diseases), Rhombomys opimus (3 diseases), Cricetulus migratorius (3 diseases), and Nesokia indica (2 diseases).

Conclusions/Significance

The results of this review indicate the importance of rodent-borne diseases in Iran. Considering notable diversity of rodents and their extensive distribution throughout the country, it is crucial to pay more attention to their role in spreading infectious diseases for better control of the diseases.

This review showed that approximately half of the known rodent-borne diseases have been reported in Iran, half of which were reported both in humans and rodents. Most of the diseases were bacterial and parasitic. Plague, leishmaniasis, and hymenolepiasis were the most frequent diseases among rodent populations. Also, this review showed that among the rodent species, three commensal ones—R. norvegicus, M. musculus, and R. rattus—play an important role in the transmission of diseases to humans in Iran. Considering repeated reports of many of these diseases in humans and rodents, and the notable diversity and extensive distribution of rodents throughout Iran, it is crucial to pay adequate attention to rodents as a source of zoonotic infectious diseases in the country.